local/global alignment

[lichy]

hi,

how to make local/global alignment by using perl.

i dont need the code for the time being, just need step by step methods to do so.

thanks for the help.

[NeedHelp]

What is a local/global alignment?

[KevinADC]

local() is a builtin perl function that defines a global perl variable with a temporary value inside a block of code. For example, "$/" is a global perl variable, you would use local() to temporarily change it's value:

here $/ has its default value

sub do_this {
   local $/ = "\n\n";
   .....
}

here $/ has it's default value again

[lichy]

Originally Posted by KevinADC

local() is a builtin perl function that defines a global perl variable with a temporary value inside a block of code. For example, "$/" is a global perl variable, you would use local() to temporarily change it's value:

here $/ has its default value

sub do_this {
   local $/ = "\n\n";
   .....
}

here $/ has it's default value again

wah! eh... can explain in detail? sorry about that. my knowledge in perl is very litmited.

[KevinADC]

I am not even sure I know what your original question was because there is no such thing as "alignment" that I know of. I assumed you were asking about global or local scope of perls global variables, but maybe I have assumed wrongly. Please clarify your original question.

[lichy]

oh i'm sorry.

eh local/global alignment, is actually like a matching strings.

for example

user input two strings

1st string: AGTTCAGCA

2nd string: ATCATCA

after some programming using perl language,

the output will become

AGTTCAGCA
A- T -CATCA

the best result.

i have no idea how to program it.

[KevinADC]

I guess you mean local/global in terms of DNA and not perl? I have told you previously my personal policy for helping students, I will not help with code unless you post some code that shows an honest effort at solving the problem first.

[lichy]

no, i think you get the wrong idea. i'm not here for codes or whatsoever.

i just need someone to help me by breaking down this programming into simpler parts.

cause the situation now is that i dont even know how to start.

i dont know how to calculate it to achieve the result here.

and yes, it's local/global alignment for dna. sorry for not clarifying that previously.

[KevinADC]

Well, I don't know what local/global alignment in DNA terms is. You posted two strings and a final output, but I have no idea what the algorithim or criteria is for acheiving the final output based on the input. Have you ever looked into bioperl?

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